ABCdb is a

biological database Biological databases are libraries of biological sciences, collected from scientific experiments, published literature, high-throughput experiment technology, and computational analysis. They contain information from research areas including geno ...

for the adenosine triphosphate-binding cassette (ABC) transporters encoded by completely sequenced

archaea Archaea ( ) is a Domain (biology), domain of organisms. Traditionally, Archaea only included its Prokaryote, prokaryotic members, but this has since been found to be paraphyletic, as eukaryotes are known to have evolved from archaea. Even thou ...

l and

bacteria Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of Prokaryote, prokaryotic microorganisms. Typically a few micr ...

genome A genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as ...

s. These

proteins Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, re ...

are important for transporting substances into cells and are found in all living organisms.

biological function of ABC systems

Most ABC systems function in the transport of a compound across a membrane into the cell (importer) or to the exterior (exporter), for which the system generates energy by the

hydrolysis Hydrolysis (; ) is any chemical reaction in which a molecule of water breaks one or more chemical bonds. The term is used broadly for substitution reaction, substitution, elimination reaction, elimination, and solvation reactions in which water ...

of adenosine triphosphate (ATP). The ABC transporters occur in all living organisms. An ABC transporter system consist minimally of two components: an ATP binding cassette and a transmembrane domain or membrane spanning domain. These are usually separate

protein Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...

s or can occur as

protein domain In molecular biology, a protein domain is a region of a protein's Peptide, polypeptide chain that is self-stabilizing and that Protein folding, folds independently from the rest. Each domain forms a compact folded Protein tertiary structure, thre ...

s. A typical ABC transporter is composed of two nucleotide binding domains that energize transport via ATP hydrolysis and of two membrane spanning domains that act as a membrane channel for the substrate. Importers require a solute binding protein that recognizes and binds the substrate. The different partners of an ABC system are generally encoded by neighboring genes.

Features

The ABC proteins form a

protein superfamily A protein superfamily is the largest grouping (clade) of proteins for which common ancestry can be inferred (see homology (biology), homology). Usually this common ancestry is inferred from structural alignment and mechanistic similarity, even if n ...

encoded by large families of paralogous genes.

Sequence analysis In bioinformatics, sequence analysis is the process of subjecting a DNA, RNA or peptide sequence to any of a wide range of analytical methods to understand its features, function, structure, or evolution. It can be performed on the entire genome ...

shows that members of the ABC superfamily may have diverged from common ancestral forms and permits to organize ABC proteins into sub-families. The classification of ABC systems into (sub-)families can help to predict which substrates may be transported by the system. ABCdb is a public resource, from which one can: * select a strain from the tree of

species A species () is often defined as the largest group of organisms in which any two individuals of the appropriate sexes or mating types can produce fertile offspring, typically by sexual reproduction. It is the basic unit of Taxonomy (biology), ...

and view all its ABC systems, classified into (sub-)families. * for a particular ABC (sub-)family, compare all the proteins of completely sequenced prokaryotes. * use a protein sequence and blast it against ABCdb to find annotations for similar proteins

References

{{reflist

External links

* http://www-abcdb.biotoul.fr/ ABCdb website ATP-binding cassette transporters Protein databases Protein classification Education in Toulouse

biological function of ABC systems

Features

See also

References

External links